lib/src1/bruker2dicom.cxx

   1 #include "bruker2dicom.h"
   2 #include <boost/filesystem/path.hpp>
   3 #include <boost/filesystem/operations.hpp>
   4 #include "brukerexception.h"
   5
   6 #ifndef PATH_MAX // If not defined yet : do it
   7    #define PATH_MAX 2048
   8 #endif
   9
  10 bool Bruker2Dicom::Execute()
  11 {
  12    // ----- Check input directory name -----
  13
  14    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  15
  16    //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
  17    if ( ! boost::filesystem::is_directory(InputDirName) )
  18    {
  19       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
  20       return 0;
  21    }
  22    else
  23    {
  24       if (verbose)
  25          std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
  26    }
  27
  28    // ----- Check output directory name -----
  29
  30    std::string strDirNameOut(OutputDirName);
  31    bool res=CreateDirectory(strDirNameOut);
  32    if (!res) {
  33       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
  34       //exit (0);
  35       throw ( BrukerHopelessException ("Output directory creation failure "));
  36    }
  37
  38    std::string strDirNamein(InputDirName);
  39    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
  40    std::string strDirNameout(OutputDirName);
  41
  42 /*
  43    if (listonly)
  44    {
  45       std::cout << "------------List of found files ------------" << std::endl;
  46       dirList.Print();
  47       std::cout << std::endl;
  48       return 1;
  49    }
  50 */
  51
  52 //
  53 // e.g : at level 0, in : B67d1.Bp1
  54 //
  55 //           1  2  3  4  5  6  AdjStatePerStudy  subject
  56 //
  57
  58    GDCM_NAME_SPACE::DirListType fileNames;
  59    fileNames = dirList.GetFilenames();
  60    bool canOpen;
  61    std::string outputFileName;
  62
  63   // BrukerDataSet br_subject;
  64    std::string subject;
  65    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
  66              GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
  67              "subject";
  68    if (verbose)
  69         std::cout << " Subject : [" <<  subject << "]" << std::endl;
  70
  71    bool subjectFound;
  72    canOpen =br_subject.LoadFile(subject);
  73    if (!canOpen)
  74    {
  75       //std::cout << "Hopeless! no 'subject' found" << std::endl;
  76       //throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
  77
  78       std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl;
  79       subjectFound = false;
  80    }
  81    else
  82    {
  83       br_subject.FillMap();
  84       subjectFound = true;
  85    }
  86    //br_subject.PrintSelf();
  87
  88   // get info for 'Study Description'
  89
  90     if (subjectFound)
  91     {
  92        BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
  93        subject_name = b_name.GetStringValue()[0];
  94        strPatientName = subject_name;
  95        cleanString(subject_name);
  96      }
  97      else
  98         subject_name ="defaultPatName";
  99
 100     // creation directory : 'nom du patient'
 101     std::string tempStringPatDir(OutputDirName);
 102     tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
 103
 104     res=CreateDirectory(tempStringPatDir);
 105     if (!res) {
 106        std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
 107        throw ( BrukerHopelessException ("Patient directory creation failure "));
 108     }
 109
 110     std::string subject_entry;
 111     std::string subject_position;
 112     std::string subject_date;
 113     std::string subject_study_name;
 114
 115     if (subjectFound)
 116     {
 117        BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
 118        subject_entry = b_entry.GetStringValue()[0];
 119        //cleanString(subject_entry);
 120        subject_entry = subject_entry.substr(11, subject_entry.size()-11);
 121
 122        BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
 123        subject_position = b_position.GetStringValue()[0];
 124        //cleanString(subject_position);
 125        subject_position = subject_position.substr(9, subject_position.size()-9);
 126
 127        BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
 128        subject_date = b_date.GetStringValue()[0];
 129        strStudyTimeDate = subject_date;
 130        cleanString(subject_date);
 131
 132        BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
 133        subject_study_name = b_study_name.GetStringValue()[0];
 134        subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
 135        cleanString(subject_study_name);
 136    }
 137    else  // Desperate trick when file 'subject' is missing
 138    {
 139       subject_entry      = "HeadFirst";            // Why not?
 140       subject_position   = "Supine";               // Why not?
 141       strStudyTimeDate   = "06_06_06_6_June_1666"; // Why not?
 142       subject_date       = "6_June_1666";          // Why not?
 143       subject_study_name = "defStudyName";         // Why not?
 144    }
 145     // subject_name is already in 'Patient Name'
 146     strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
 147
 148     // creation directory : 'nom de la Study'
 149
 150     std::string tempStringStudyDir(OutputDirName);
 151     tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
 152
 153     res=CreateDirectory(tempStringStudyDir);
 154     if (!res) {
 155        std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
 156        throw ( BrukerHopelessException ("Study directory creation failure "));
 157     }
 158
 159    char outputDirName[(unsigned int) PATH_MAX+2];
 160
 161    strStudyUID    = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 162    serieNumber    = 0;
 163    instanceNumber = 0;
 164
 165    // -----------------------------------------------------
 166    // Iterate to ALL the objets(files/directories) found in the input directory
 167    // (this is level ZERO)
 168    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
 169    // -----------------------------------------------------
 170
 171    GDCM_NAME_SPACE::DirListType::iterator it;
 172
 173    for (it = fileNames.begin();
 174          it != fileNames.end();
 175        ++it)
 176    {
 177       if ( boost::filesystem::is_directory(*it) )
 178       {
 179          if (verbose)
 180             std::cout << "[" << *it << "] is a directory" << std::endl;
 181
 182          if((*it) == "AdjStatePerStudy")  // avoid trouble with new version 'AdjStatePerStudy' directory
 183             continue;
 184
 185          //BrukerDataSet br_acqp;
 186          std::string strAcqp;
 187          strAcqp = (*it) +
 188                    GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 189                    "acqp";
 190
 191          br_acqp.LoadFile(strAcqp);
 192          br_acqp.FillMap();
 193
 194 //std::cout << "out of br_acqp.FillMap " << std::endl;
 195          std::string acqp_scan_name;
 196          std::string acqp_method;
 197          std::string acqp_protocol_location;
 198
 199          BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
 200          acqp_protocol_location = b_protocol_location.GetStringValue()[0];
 201          cleanString(acqp_protocol_location);
 202
 203 //std::cout << "out of br_acqp.FillMap 1" << std::endl;
 204          BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
 205 //std::cout << "out of br_acqp.FillMap 11" << std::endl;
 206          acqp_scan_name = b_scan_name.GetStringValue()[0];
 207 //std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl;
 208          cleanString(acqp_scan_name);
 209 //std::cout << "out of br_acqp.FillMap 2" << std::endl;
 210          BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
 211          b_method.PrintSelf();
 212          acqp_method = b_method.GetStringValue()[0];
 213
 214          cleanString(acqp_method);
 215 //std::cout << "out of br_acqp.FillMap 3" << std::endl;
 216          BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
 217 //std::cout << "out of br_acqp.FillMap 4" << std::endl;
 218          //b_list_size.PrintSelf(); //JP
 219
 220          nbSlices =  b_list_size.GetIntValue()[0];
 221 //std::cout << "out of br_acqp.FillMap 5" << std::endl;
 222          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
 223                        /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
 224                          + "." + acqp_scan_name
 225                          + "." + acqp_method.c_str();
 226
 227          sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),                //OutputDirName.c_str(),
 228                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 229                           strSerieDescr.c_str() );
 230
 231          std::cout << " ================================================================================\n"
 232                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
 233                    << " ================================================================================"
 234                    << std::endl;
 235
 236         if (verbose)
 237            printf ("outputDirName [%s]\n", outputDirName);
 238         try {
 239            DealWithNiveau1(*it, outputDirName);
 240         }
 241         catch (BrukerHopelessException &e)
 242         {
 243          std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
 244          continue;
 245         }
 246       }
 247    } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
 248 }
 249
 250 // =====================================================================
 251
 252 void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
 253 //
 254 // e.g. : at level 1, in B67d1.Bp1/6
 255 //
 256 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 257
 258    bool res = CreateDirectory(currentOutputDirName);
 259
 260    if (!res) {
 261       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 262       throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
 263      // exit (0);
 264    }
 265    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
 266    GDCM_NAME_SPACE::DirListType fileNames;
 267    fileNames = dirList.GetFilenames();
 268    // -----------------------------------------------------
 269    // Iterate to ALL the objets(files/directories) found in the input directory
 270    // -----------------------------------------------------
 271    GDCM_NAME_SPACE::DirListType::iterator it;
 272
 273    for (it = fileNames.begin();
 274         it != fileNames.end();
 275       ++it)
 276    {
 277       if ( boost::filesystem::is_regular(*it) )
 278       //if ( ! boost::filesystem::is_directory(*it) )
 279       {
 280          if (verbose)
 281             std::cout << "--- [" << *it << "] is a file." << std::endl;
 282       }
 283    }
 284
 285    char outputDirName[(unsigned int) PATH_MAX+2];
 286    //std::string firstName;
 287    bool canOpen;
 288    for (it = fileNames.begin();
 289         it != fileNames.end();
 290       ++it)
 291    {
 292       if ( boost::filesystem::is_directory(*it) )
 293       {
 294          // will be always "pdata" ...
 295          if (verbose)
 296             std::cout << "--- [" << *it << "] is a directory" << std::endl;
 297
 298               /* a recuperer :
 299               if (FileLine.startsWith("##$ACQ_size=")) {
 300               if (FileLine.startsWith("##$NI=")) {
 301               if (FileLine.startsWith("##$NR=")) {
 302               if (FileLine.startsWith("##$ACQ_obj_order=")) {
 303               if (FileLine.startsWith("##$ACQ_word_size=")) {
 304               if (FileLine.startsWith("##$BYTORDA=")) {
 305               if (FileLine.startsWith("##$PULPROG=")) {
 306               */
 307
 308          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 309                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 310                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
 311          //br1.PrintSelf();
 312
 313           std::string strMethod;
 314           //std::string firstName = *(fileNames.begin());
 315
 316           strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
 317                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 318                       "method";
 319             // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
 320           canOpen = br_method.LoadFile(strMethod);
 321           if (!canOpen)
 322           {
 323              strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 324                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 325                          "imnd";
 326              //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
 327              canOpen = br_method.LoadFile(strMethod);
 328              if (!canOpen)
 329              {
 330                 std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
 331                           << level1Directory  << "]; we skip it!" << std::endl;
 332                 continue;
 333                 //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
 334                 //exit(0);  /// \TODO throw an exception !
 335              }
 336           }
 337           if (verbose)
 338              std::cout << "open => [" << strMethod << "] successfully" << std::endl;
 339           br_method.FillMap();
 340
 341           /* a recuperer :
 342              ##$PVM_Fov (dimension)  // ou plutot RECO_fov !
 343           */
 344   /*
 345           dans method (pour perfusion  seulement?) :
 346           ##$PVM_ObjOrderList=( 8 )
 347           0 2 4 6 1 3 5 7
 348           ##$PVM_NSPacks=2
 349           ##$PVM_SPackArrNSlices=( 2 )
 350           7 1
 351   */
 352          try {
 353             DealWithNiveau2(*it, outputDirName);
 354          }
 355          catch (BrukerHopelessException &e)
 356          {
 357             std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
 358             continue;
 359          }
 360       }
 361    }
 362 }
 363
 364 // =====================================================================
 365
 366 void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
 367
 368 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 369 //
 370 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
 371 //
 372
 373    bool res = CreateDirectory(currentOutputDirName);
 374
 375    if (!res) {
 376       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 377       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
 378       //exit (0);
 379    }
 380
 381    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 382
 383    GDCM_NAME_SPACE::DirListType fileNames;
 384    fileNames = dirList.GetFilenames();
 385
 386    char outputDirName[(unsigned int) PATH_MAX+2];
 387
 388    // -----------------------------------------------------
 389    // Iterate to ALL the objets(files/directories) found in the input directory
 390    // -----------------------------------------------------
 391    GDCM_NAME_SPACE::DirListType::iterator it;
 392    bool canOpen;
 393
 394    if (verbose)
 395    for (it = fileNames.begin();
 396         it != fileNames.end();
 397       ++it)
 398    {
 399       if ( ! boost::filesystem::is_directory(*it) )
 400       {
 401          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
 402       }
 403    }
 404
 405    for (it = fileNames.begin();
 406          it != fileNames.end();
 407        ++it)
 408    {
 409       if ( boost::filesystem::is_directory(*it) )
 410       {
 411
 412          if (verbose)
 413             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
 414
 415         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 416         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 417         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 418   // MUST be 'pdata'!
 419
 420 //
 421 // (interest of previous method :
 422 // If unaware user changed the pdata name, it goes on working
 423 //
 424           std::string str_isa;
 425           str_isa = (*it) +
 426                     GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 427                    "isa";
 428
 429           std::string str_isa_func_name;
 430           canOpen = br_isa.LoadFile(str_isa);
 431           if (!canOpen)
 432           {
 433              sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
 434                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 435                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
 436           }
 437           else
 438           {
 439              br_isa.FillMap();
 440              BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
 441
 442              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
 443              cleanString(str_isa_func_name);
 444
 445              sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(),
 446                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
 447                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
 448              str_isa_func_name.c_str());
 449           }
 450           try {
 451              DealWithNiveau3(*it, outputDirName);
 452           }
 453           catch (BrukerHopelessException &e)
 454           {
 455              std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 456                        << " We skip [" << level2Directory << "]" << std::endl;
 457              continue;
 458           }
 459           catch (BrukerInitException &e)
 460           {
 461              std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
 462                        << " We skip [" << level2Directory << "]" << std::endl;
 463              continue;
 464           }
 465       }
 466    }
 467 }
 468
 469 //
 470 // =====================================================================
 471 //
 472
 473 void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
 474
 475 //
 476 // e.g. at level 3, in
 477
 478    // just to be able to go on checking // JP
 479    if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
 480       return;
 481
 482    bool res = CreateDirectory(currentOutputDirName);
 483
 484    if (!res)
 485    {
 486       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 487       throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
 488       //exit (0);
 489    }
 490
 491    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
 492    GDCM_NAME_SPACE::DirListType::iterator it;
 493    GDCM_NAME_SPACE::DirListType fileNames;
 494    fileNames = dirList.GetFilenames();
 495
 496    char original2dseqName       [(unsigned int) PATH_MAX+2];
 497    char original2dseqName_XXX   [(unsigned int) PATH_MAX+2];
 498    char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
 499
 500    char outputMhdFileName       [(unsigned int) PATH_MAX+2];
 501    char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
 502    char output2dseqName         [(unsigned int) PATH_MAX+6];
 503    char output2dseqCartoName    [(unsigned int) PATH_MAX+6];
 504
 505    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
 506    bool canOpen;
 507
 508    //-------------- try d3proc;
 509    char char_d3proc[(unsigned int) PATH_MAX+2];
 510
 511    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
 512
 513    if (verbose)
 514       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
 515    std::string str_d3proc(char_d3proc);
 516    canOpen = br_d3proc.LoadFile(str_d3proc);
 517
 518    if (!canOpen)
 519    {
 520       std::cout << "Hopeless! no 'd3proc' found" << std::endl;
 521       throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
 522       //exit(0);  /// \TODO throw an exception !
 523    }
 524
 525    canOpen = br_d3proc.FillMap();
 526    if (!canOpen)
 527    {
 528       std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
 529       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
 530       //exit(0);  /// \TODO throw an exception !
 531    }
 532
 533    //-------------- end try d3proc;
 534
 535
 536  // -------------------try reco
 537
 538    char char_reco[(unsigned int) PATH_MAX+2];
 539
 540    sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 541     //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
 542     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
 543     //             "d3proc";
 544    if (verbose)
 545       std::cout << "reco: --- => [" << char_reco << "]" << std::endl;
 546
 547    std::string str_reco(char_reco);
 548    canOpen = br_reco.LoadFile(str_reco);
 549
 550    if (!canOpen) // we try in directory ../1
 551    {
 552       if (verbose)
 553          std::cout << "[" << str_reco << "] not found " << std::endl;
 554       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
 555       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
 556       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
 557       //str_reco=char_reco;
 558       canOpen = br_reco.LoadFile(str_reco);
 559       if (!canOpen)
 560       {
 561          std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;
 562          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
 563          //exit(0);  /// \TODO throw an exception !
 564       }
 565    } else {
 566       if (verbose)
 567          std::cout << "[" << str_reco << "] successfully Loaded " << std::endl;
 568    }
 569
 570    canOpen = br_reco.FillMap();
 571    if (!canOpen)
 572    {
 573       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
 574       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
 575       //exit(0);  /// \TODO throw an exception !
 576    } else {
 577       if (verbose)
 578          std::cout << "[" << str_reco << "] successfully Mapped" << std::endl;
 579    }
 580
 581    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 582    // br_reco.PrintSelf();
 583    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
 584    // -------------------end try reco
 585
 586
 587    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
 588    int NX = bX.GetIntValue()[0];
 589
 590    if (verbose)
 591       std::cout << "IM_SIX " << NX << std::endl;
 592    BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
 593    int NY = bY.GetIntValue()[0];
 594
 595    if (verbose)
 596          std::cout << "IM_SIY " << NY << std::endl;
 597    /// \todo : check if there are actually 3 dimensions or only 2
 598
 599    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
 600    int nbFrames = bZ.GetIntValue()[0];
 601    if (verbose)
 602          std::cout << "IM_SIZ " << nbFrames << std::endl;
 603
 604         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
 605
 606    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
 607
 608    std::string mhdDataPixelType;
 609    int pixelSize;
 610    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
 611
 612
 613  /*
 614
 615  // See mail Denis :
 616  // En regle generale il vaut mieux que l'on passe par RECO_*
 617  // pour extraire les parametres de l'image
 618  //
 619
 620    BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
 621    double fovX = fov.GetDoubleValue()[0];
 622    double fovY = fov.GetDoubleValue()[1];
 623    if (verbose)
 624       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 625
 626    BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
 627    double spatResolX = spatResol.GetDoubleValue()[0];
 628    double spatResolY = spatResol.GetDoubleValue()[1];
 629    if (verbose)
 630       std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
 631
 632 */
 633
 634 /* ------  */
 635 // Better we use 'get' accessors from BrukerImage class, as Denis wrote them
 636
 637    BrukerFieldData fov = br_reco.GetFieldData("RECO_fov");
 638    double fovX = fov.GetDoubleValue()[0];
 639    double fovY = fov.GetDoubleValue()[1];
 640    if (verbose)
 641       std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl;
 642
 643    BrukerFieldData size = br_reco.GetFieldData("RECO_size");
 644    double sizeX = size.GetDoubleValue()[0];
 645    double sizeY = size.GetDoubleValue()[1];
 646
 647    if (verbose)
 648       std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl;
 649
 650    double spatResolX = fovX / sizeX;
 651    double spatResolY = fovY / sizeY;
 652
 653    if (verbose)
 654       std::cout << "spatResol (ds reco : fov/size) " << spatResolX << " " << spatResolY << std::endl;
 655
 656 /* ------  */
 657
 658    /// \TODO probabely a more sophisticated accessor will be necessary :
 659    ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
 660
 661    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
 662    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 663
 664    if (verbose)
 665       std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl;
 666
 667 // ----------------------------------------------------------------------------------------
 668
 669    if (mhd)
 670    {
 671       sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
 672                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
 673       res = CreateDirectory( currentOutputMhdDirName );
 674       if (!res) {
 675          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
 676          throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
 677          //exit (0);
 678       }
 679
 680       if (verbose)
 681          std::cout << "Directory creation [" <<  currentOutputDirName << "]" << std::endl;
 682    }  // end if mhd
 683
 684    if (verbose)
 685          std::cout << "nbFrames " << nbFrames << std::endl;
 686    if (verbose)
 687          std::cout << "nbSlices " << nbSlices << std::endl;
 688    int k;
 689    int nbInstants = nbFrames/nbSlices;
 690    if (verbose)
 691          std::cout << "nbInstants (deduced)" << nbInstants << std::endl;
 692    int instantNb;
 693    int sliceNb;
 694    FILE *fp;  // for MHD files
 695
 696    sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
 697
 698 /**/
 699   // \TODO : tenir compte du bazar precedent
 700
 701     // load 2dseq in memory
 702
 703    fp = fopen(original2dseqName, "rb");
 704    if (!fp)
 705    {
 706       // try 2dseq_Angio2D ?!?
 707
 708       sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
 709       fp = fopen(original2dseqName_XXX, "rb");
 710       if (!fp)
 711       {
 712          std::cout << "Cannot open [" << original2dseqName << "] nor [" <<  original2dseqName_XXX << "] for reading" << std::endl;
 713          fclose(fp);
 714          throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
 715          //exit (0);
 716       }
 717    }
 718
 719    unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
 720    ///\ TODO : find a safer way to be sure to read everything!
 721    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 722
 723    // This one will be important!
 724    // ---------------------------
 725    try {
 726       imageSet = CreateImageSet ( );
 727    }
 728    catch (BrukerInitException& e)
 729    {
 730       if (verbose)
 731          std::cout <<  "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
 732                    <<  "catched in DealWithNiveau3" << std::endl;
 733       //return;
 734       throw (e);
 735    }
 736
 737    serieNumber++;
 738    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 739    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
 740    {
 741        if (verbose)
 742           std::cout << "Single instant : do not split" << std::endl;
 743        if (mhd)
 744        {
 745              sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
 746                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 747              fp=fopen(outputMhdFileName, "w");
 748              if (!fp)
 749              {
 750                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 751                 throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 752                 //exit(0);
 753              }
 754              else
 755              {
 756                fprintf(fp, "ObjectType = Image\n");
 757                fprintf(fp, "NDims = 3\n" );
 758                fprintf(fp, "BinaryData = True \n" );
 759                fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 760                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
 761                fprintf(fp, "HeaderSize = %d\n", 0);
 762                //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
 763                fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
 764                fprintf(fp, "Position = 0 0 %d\n", 0 );
 765                fprintf(fp, "Offset = 0 0 0\n" );
 766                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 767                fprintf(fp, "ElementNumberOfChannels = 1\n" );
 768                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 769                fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
 770                fclose(fp);
 771              }
 772              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
 773                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 774              fp=fopen(output2dseqSliceFileName, "wb");
 775              if (!fp)
 776              {
 777                 std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 778                 throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
 779              }
 780              else
 781              {
 782                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
 783              }
 784              fclose(fp);
 785              serieNumber ++;
 786              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
 787        }  // end if mhd
 788        if (dicom)
 789        {
 790              sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
 791                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 792
 793             /* ----------- Write Dicom Image  ---------------*/
 794              MakeDicomImage(buffer_2dseq,
 795                NX,
 796                NY,
 797                nbFrames,
 798                pixelSize,
 799                //fovX/NY, fovY/NY, sliceDistance,
 800                spatResolX, spatResolY, sliceDistance,
 801                output2dseqSliceFileName,
 802                subject_name,
 803                day,
 804                strStudyUID,
 805                strSerieUID,
 806                strStudyDescr,
 807                strSerieDescr,
 808                strStudyTimeDate,
 809                0,// index frame number
 810                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 811              );
 812        }  // end if dicom
 813    }  // end if nbInstants = 1
 814
 815    else  // more than ONE instant
 816    {
 817           // Interleaved !
 818           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 819          unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 820
 821          k = 0;
 822          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
 823          {
 824             if (mhd)
 825             {
 826                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
 827                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
 828                if (verbose)
 829                   std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
 830                fp=fopen(outputMhdFileName, "w");
 831                if (!fp)
 832                {
 833                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
 834                    throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
 835                    //exit(0);
 836                }
 837                else
 838                {
 839             /* ----------- Write MHD Image  ---------------*/
 840                 //if (verbose)
 841                 //   std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
 842                    fprintf(fp, "ObjectType = Image\n");
 843                    fprintf(fp, "NDims = 3\n" );
 844                    fprintf(fp, "BinaryData = True \n" );
 845                    fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
 846                    fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
 847                    fprintf(fp, "HeaderSize = %d\n", 0);
 848                    //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
 849                    fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
 850                    fprintf(fp, "Position = 0 0 %d\n", sliceNb );
 851                    fprintf(fp, "Offset = 0 0 0\n" );
 852                    fprintf(fp, "CenterOfRotation = 0 0 0\n" );
 853                    fprintf(fp, "ElementNumberOfChannels = 1\n" );
 854                    fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
 855                    fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
 856                    fclose(fp);
 857                } // end write MHD
 858
 859                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
 860                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
 861                fp=fopen(output2dseqSliceFileName, "wb");
 862                if (!fp)
 863                {
 864                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 865                    throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
 866                    //exit (0);
 867                }
 868                int frameSize = NX*NY*pixelSize;
 869                for (instantNb=0; instantNb<nbInstants; instantNb++)
 870                {
 871 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 872                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 873                             frameSize,
 874                             1, fp);
 875                }
 876                fclose(fp);
 877 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
 878             }  // end if mhd
 879
 880             if (dicom)
 881             {
 882                // desperate try !
 883              /*
 884                sprintf(output2dseqSliceFileName, "%sdummy_buffer",
 885                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
 886                fp=fopen(output2dseqSliceFileName, "wb");
 887                if (!fp)
 888                {
 889                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
 890                    exit (0);
 891                }
 892                int frameSize = NX*NY*pixelSize;
 893                for (instantNb=0; instantNb<nbInstants; instantNb++)
 894                {
 895 // std::cout << "------------SN " << sliceNb << " IN " << instantNb <<  " T " << nbSlices*instantNb + sliceNb << std::endl;
 896                     fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
 897                             frameSize,
 898                             1, fp);
 899                }
 900                fclose(fp);
 901
 902                fp=fopen(output2dseqSliceFileName, "rb");
 903                if (!fp)
 904                {
 905                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
 906                    exit (0);
 907                }
 908                fread( pixelsForCurrentSlice,
 909                             frameSize*nbInstants,
 910                             1, fp);
 911                fclose(fp);
 912               // end of desperate try !
 913               */
 914
 915                /* ----------- Write Dicom Image  ---------------*/
 916
 917                int frameSize = NX*NY*pixelSize;
 918                for (instantNb=0; instantNb<nbInstants; instantNb++)
 919                {
 920                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
 921                }
 922
 923                int indOfFirsImageWithinImageSet =  nbSlices*instantNb;
 924                sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
 925                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
 926
 927                MakeDicomImage(
 928                   pixelsForCurrentSlice,
 929                   NX,
 930                   NY,
 931                   nbInstants,
 932                   pixelSize,
 933                   spatResolX, spatResolY, sliceDistance,
 934                   //fovX/NY, fovY/NY, sliceDistance,
 935                   output2dseqSliceFileName,
 936                   subject_name,
 937                   day,
 938                   strStudyUID,
 939                   strSerieUID,
 940                   strStudyDescr,
 941                   strSerieDescr,
 942                   strStudyTimeDate,
 943                   sliceNb*nbInstants,
 944                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
 945                );
 946                if (verbose)
 947                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
 948
 949            } // en if dicom
 950
 951         k++;
 952         }
 953         delete [] pixelsForCurrentSlice;
 954      }  // end nbInstants == 1
 955    delete [] buffer_2dseq;
 956 /**/
 957
 958
 959    // -----------------------------------------------------
 960    //  deal with MatLab-generated Carto file.
 961    // -----------------------------------------------------
 962
 963    dealWithCarto(fileNames,  NX,  NY,  nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
 964                    copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
 965 }
 966
 967
 968 // ===========================================================================================
 969
 970 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
 971                                  /*double fovX, double fovY, */
 972                                  double spatResolX, double spatResolY, double sliceDistance,
 973                                  char *copyFile, std::string &currentOutputDirName,
 974                                  char *outputMhdFileName, char *output2dseqCartoName)
 975 {
 976    // -----------------------------------------------------
 977    //  deal with MatLab-generated Carto file.
 978    // -----------------------------------------------------
 979
 980    const char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
 981    const char *separator[] =  { "_", ".", "-", "" }; //  add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
 982    int icode;
 983    int iseparator;
 984    GDCM_NAME_SPACE::DirListType::iterator it;
 985    char file_name_ident[500];
 986    FILE *fp;
 987
 988    // Iterate to ALL the objets(files/directories) found in the input directory
 989    for (it = fileNames.begin();
 990         it != fileNames.end();
 991       ++it)
 992    {
 993       if ( boost::filesystem::is_regular(*it) )
 994       //if ( ! boost::filesystem::is_directory(*it) )
 995       {
 996          if (verbose)
 997             std::cout << "--- [" << *it << "] is a file..." << std::endl;
 998
 999          icode      = 0;
1000          while (code[icode][0] != 0)
1001          {
1002          iseparator = 0;
1003          while (separator[iseparator][0] != 0)
1004          {
1005             sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g  "2dseq_ADC"
1006             //if (verbose)
1007             //   std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
1008             std::string::size_type loc = (*it).rfind(file_name_ident);
1009
1010             if ( loc != std::string::npos )
1011             {
1012
1013        ///\ TODO : find a safer way to be sure to read everything!
1014               unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
1015               fp = fopen ( (*it).c_str(), "rb");
1016               if (!fp){
1017                  std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
1018                  throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
1019                }
1020                fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
1021
1022                     // ?!?  sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1023                std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
1024                          << NX*NY*sizeof(double)*nbSlices << std::endl;
1025                std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
1026                if (mhd)
1027                {
1028                   // Copy the data file in the new directory
1029                   sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
1030                             currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
1031                   system(copyFile);
1032                   sprintf(outputMhdFileName, "%s%c%s%s",
1033                                          currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
1034                   if (verbose)
1035                     std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1036
1037                   FILE *fp;
1038                   fp=fopen(outputMhdFileName, "w");
1039                   if (!fp)
1040                   {
1041                      std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
1042                   }
1043                   else
1044                   {
1045                      fprintf(fp, "ObjectType = Image\n");
1046                      fprintf(fp, "NDims = 3\n" );
1047                      fprintf(fp, "BinaryData = True \n" );
1048                      fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
1049                      fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
1050                      fprintf(fp, "HeaderSize = %d\n", 0 );
1051                      fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance );
1052                      fprintf(fp, "Position = 0 0 0\n" );
1053                      fprintf(fp, "Offset = 0 0 0\n" );
1054                      fprintf(fp, "CenterOfRotation = 0 0 0\n" );
1055                      fprintf(fp, "ElementNumberOfChannels = 1\n" );
1056                      fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
1057                      fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
1058
1059                      fclose(fp);
1060                   }
1061                   if (verbose)
1062                      std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
1063                }  // end if mhd
1064
1065             // ----------- Write Dicom Image  ---------------
1066
1067                if (dicom)
1068                {
1069                   sprintf(output2dseqCartoName, "%s%c%s%s",
1070                                        currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
1071                   if (verbose)
1072                      std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
1073
1074                   strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
1075                   std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
1076                   MakeDicomImage(buffer_carto,
1077                      NX,
1078                      NY,
1079                      nbSlices,
1080                      8, // pixelSize
1081                      //fovX/NY, fovY/NY, sliceDistance,
1082                      spatResolX, spatResolY, sliceDistance,
1083                      output2dseqCartoName,
1084                      subject_name,
1085                      day,
1086                      strStudyUID,
1087                      strSerieUID,
1088                      strStudyDescr,
1089                      strNewSerieDescr,
1090                      strStudyTimeDate,
1091                      0,
1092                      GDCM_NAME_SPACE::CREATED_IMAGE
1093                   );
1094                }  // end if dicom
1095
1096                delete [] buffer_carto;
1097                if (verbose)
1098                   std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
1099                break; // don't check for more ident on same file name!
1100
1101             }  // end deal with _ADC, -adc, etc
1102           iseparator ++;
1103           }  // end iterate speparators
1104           icode++;
1105           } // end iterate code
1106       } // end boost::filesystem::is_regular(*it)
1107    } // end iterate on all objects (files, dir, etc)
1108 } // end method
1109
1110
1111 // ==========================================================================================================
1112
1113 bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
1114 {
1115    std::string systemCommand;
1116
1117    if (verbose)
1118       std::cout << "Check for output directory :[" << OutputDirName << "]."
1119                 <<std::endl;
1120    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
1121    {
1122       std::string strDirNameout(OutputDirName);        // to please gcc 4
1123       systemCommand = "mkdir " + strDirNameout;        // create it!
1124       if (verbose)
1125          std::cout << systemCommand << std::endl;
1126       system (systemCommand.c_str());
1127       if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
1128       {
1129          if (verbose)
1130             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
1131          //return 0;
1132          throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
1133       }
1134       else
1135       {
1136          if (verbose)
1137            std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
1138       }
1139    }
1140    else
1141    {
1142        if (verbose)
1143             std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
1144    }
1145
1146    return 1;
1147
1148 }
1149
1150
1151 // ===========================================================================================
1152
1153 /// \TODO move cleanString to 'crea' ?
1154
1155 void Bruker2Dicom::cleanString(std::string &s)
1156 {
1157    int l = s.size();
1158    if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
1159    {
1160       l--;
1161       s = s.substr(0, l);
1162    }
1163    if (s[l-1] == ' ' ) // blank space
1164    {
1165       l--;
1166       s = s.substr(0, l);
1167    }
1168
1169    if (s[0] == '<')
1170       s= s.substr(1,l-2);
1171    std::string repChar("_");
1172    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
1173 }
1174
1175
1176
1177 // ===========================================================================================
1178
1179
1180 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
1181 {
1182    if(bDPT.GetDataType() == "string")
1183    {
1184          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
1185          if (verbose)
1186             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1187          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1188
1189          if (brukerDataPixelType ==  "ip_short") {
1190             mhdDataPixelType = "MET_USHORT";
1191             pixelSize = 2;
1192          }
1193          if (brukerDataPixelType ==  "ip_int") {
1194             mhdDataPixelType = "MET_UINT";
1195             pixelSize = 4;
1196          }
1197          if (brukerDataPixelType ==  "ip_char") {
1198              mhdDataPixelType = "MET_UCHAR";
1199              pixelSize = 1;
1200          }
1201                   /// \TODO : finish the list
1202     /*
1203     case 0 : fp << "ElementType = MET_CHAR" << std::endl;
1204       break;
1205     case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
1206       break;
1207     case 2 : fp << "ElementType = MET_SHORT" << std::endl;
1208       break;
1209     case 3 : fp << "ElementType = MET_USHORT" << std::endl;
1210       break;
1211     case 4 : fp << "ElementType = MET_INT" << std::endl;
1212       break;
1213     case 5 : fp << "ElementType = MET_UINT" << std::endl;
1214       break;
1215     case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
1216       break;
1217     case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
1218     */
1219     }
1220     else
1221     {
1222          int brukerDataPixelType = bDPT.GetIntValue()[0];
1223          if (verbose)
1224             std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
1225          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
1226
1227 // Cross your fingers !!!
1228
1229 // pb : found values : 2, 3, 5
1230
1231          if (brukerDataPixelType ==  2) {
1232             mhdDataPixelType = "MET_USHORT";
1233             pixelSize = 2;
1234          }
1235          if (brukerDataPixelType ==  3) {
1236             mhdDataPixelType = "MET_USHORT";
1237             pixelSize = 2;
1238          }
1239          if (brukerDataPixelType ==  1) {
1240             mhdDataPixelType = "MET_UCHAR";
1241             pixelSize = 1;
1242          }
1243     }
1244 }
1245
1246 // ===========================================================================================
1247
1248 std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
1249 {
1250          std::vector<BrukerImage> imageSet;
1251          br_acqp.SetLoopStructure();
1252          std::vector<int> tempVect                      = br_acqp.GetLoopStructure() ;
1253          std::map<std::string, BrukerFieldData> map     = br_acqp.GetBrukerHeaderMap();
1254
1255          bool result                                    = br_acqp.ObjectVaryingProperties.init(map,tempVect);
1256
1257          if (result == false)
1258          {
1259             throw ( BrukerInitException  ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
1260          }
1261
1262          br_acqp.SetImageLoopStructure();
1263          br_acqp.SetBrukerImageList();
1264          std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
1265
1266          BrukerImage image(br_acqp,br_reco);
1267          image.Init(br_acqp,br_reco,1);
1268
1269          for(int i=0;i<brukerImageList.size();i++)
1270          {
1271             image.Init(br_acqp,br_reco,i);
1272             imageSet.push_back(image);
1273          }
1274
1275  // Just for checking
1276  /*
1277
1278          std::vector<std::vector <double> > imageOrientation;
1279          std::vector <double> imagePosition;
1280          for(int i=0;i<brukerImageList.size();i++)
1281          {
1282            // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
1283
1284            imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
1285            std::cout << "Position " << imagePosition[0] << " "
1286                      << imagePosition[1] << " "  << imagePosition[2] ;
1287            imageOrientation =  imageSet[i].getRotationMatrixRPS2XYZ();
1288            std::cout << "\t  Orientation " ;
1289            for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
1290               std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
1291
1292            //std::cout << "\t  Abs Time " << imageSet[i].getAbsoluteTimePosition();
1293            std::cout << "\t  Relat Time " << imageSet[i].getRelativeTimePosition();
1294
1295            std::cout << "\t [";
1296            for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
1297               std::cout << " " << imageSet[i].getLoopStamp()[i3];
1298            std::cout << "]" << std::endl;
1299          }
1300 */
1301    return imageSet;
1302 }
1303
1304 // ===========================================================================================
1305
1306 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
1307               int X,
1308               int Y,
1309               int nbFrames,
1310               int pixelSize,
1311               double spacingX, double spacingY, double sliceDistance,
1312               std::string dcmImageName,
1313               const std::string &patientName,
1314               const char *day,
1315               std::string &studyUID,
1316               std::string &serieUID,
1317               std::string &studyDescr,
1318               std::string &serieDescr,
1319               std::string &strStudyTimeDate,
1320               int imgNum,
1321               GDCM_NAME_SPACE::ImageContentType contentType
1322       )
1323 {
1324    std::ostringstream str;
1325
1326    GDCM_NAME_SPACE::File *file;
1327    file = GDCM_NAME_SPACE::File::New();
1328
1329   // Set the image size
1330    str.str("");
1331    str << X;
1332    file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
1333    str.str("");
1334    str << Y;
1335    file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
1336
1337    if (nbFrames != 1)
1338    {
1339       str.str("");
1340       str << nbFrames;
1341       file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
1342    }
1343
1344   // Set the pixel type
1345   //      //8, 16, 32, 64 (for double ?)
1346    str.str("");
1347    str << pixelSize*8;
1348    file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
1349
1350    file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
1351
1352    str.str("");
1353    str << pixelSize*8-1;
1354    file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
1355
1356   // Set the pixel representation // 0/1 , 0=unsigned
1357    file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
1358
1359   // Set the samples per pixel // 1:Grey level, 3:RGB
1360    file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
1361
1362 //  0028 0030 DS 2 Pixel Spacing
1363    str.str("");
1364    str << spacingX << "\\" << spacingY;
1365    file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
1366
1367  //   0018 0050 DS 1 Slice Thickness
1368    str.str("");
1369    str << sliceDistance;
1370    file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
1371
1372 //    0020 0011 IS 1 Series Number
1373    str.str("");
1374    str << serieNumber;
1375    file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
1376
1377 //    0020|0013 [IS]  [Instance Number]
1378    instanceNumber++;
1379    str.str("");
1380    str << instanceNumber;
1381    file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
1382
1383   // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
1384  //  file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1385   // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1386
1387 // OK : MR is NOT multiframe, but I want just a quick an dirty solution
1388
1389 // 1.2.840.10008.5.1.4.1.1.4         MR Image Storage
1390    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI");  // [Media Storage SOP Class UID]
1391    file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI");  // [SOP Class UID]
1392
1393   // if (strlen(patientName) != 0)
1394    file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
1395    file->InsertEntryString(patientName.c_str(),0x0010,0x0020, "LO"); // Patient's ID
1396
1397    file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
1398    file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
1399
1400 //  0008 0020 DA 1 Study Date
1401 //  0008 0030 TM 1 Study Time
1402
1403 /// \TODO split into 2 strings!
1404    file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
1405    file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),  0x0008,0x0030, "TM");
1406
1407    file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO");  // Study Description
1408    file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO");  // Series Description
1409
1410 //0008|0060 [CS] [Modality]
1411    file->InsertEntryString("MR",0x0008,0x0060, "CS");
1412
1413 // 0020 0037 DS 6 Image Orientation (Patient)
1414    char charImageOrientation[256];
1415
1416 /*
1417 std::cout << "charImageOrientation  " <<
1418                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
1419                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
1420                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
1421                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
1422                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
1423                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
1424 */
1425    sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
1426                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
1427                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
1428                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
1429                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
1430                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
1431                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
1432
1433    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
1434
1435 // 0020 0032 DS 3 Image Position (Patient)
1436
1437    char charImagePosition[256];
1438    sprintf(charImagePosition,"%f\\%f\\%f",
1439                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
1440                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
1441                              imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
1442
1443    file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");  //0020 0032 DS 3 Image Position (Patient)
1444
1445 // 0020 0x1041 DS 1 Slice Location
1446 //        sprintf(charImagePosition,"%f",float(imgNum));
1447 //        file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
1448 /*
1449   // Set Rescale Intercept
1450         str.str("");
1451         str << div;
1452         file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
1453
1454   // Set Rescale Slope
1455         str.str("");
1456         str << mini;
1457         file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
1458 */
1459
1460    GDCM_NAME_SPACE::FileHelper *fileH;
1461    fileH = GDCM_NAME_SPACE::FileHelper::New(file);
1462    fileH->SetContentType(contentType);
1463
1464    // cast is just to avoid warnings (*no* conversion is performed)
1465    //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
1466
1467 //std::cout << "--------------------------------  X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
1468
1469    fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
1470    fileH->SetWriteModeToRaw();
1471    fileH->SetWriteTypeToDcmExplVR();
1472    if( !fileH->Write(dcmImageName)) {
1473       std::cout << "Failed for [" << dcmImageName << "]\n"
1474                 << "           File is unwrittable" << std::endl;
1475       file->Delete();
1476       fileH->Delete();
1477       throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
1478    }
1479    //if (verbose)
1480    //   file->Print();
1481
1482    file->Delete();
1483    fileH->Delete();
1484 }